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CHAPTER 3 - THE MOLECUL
ES of life
WHAT WE EAT!
And..What we fart!
ORGANIC COMPOUNDS Organic Compounds contain
Carbon. Carbon is an important element
because… It forms 4 bonds.Tends to form strong
covalent bonds.
Can combine to form: single, double & triple bonds as
well as chains branches and rings.
ORGANIC COMPOUNDS
We will practice buildingthese today!
Functional groups help determine properties of organic compoundsAll are polar because oxygen or
nitrogen exert a strong pull on shared electrons
Polarity tends to make these molecules hydrophilic (water-loving)A necessity for life!
ORGANIC COMPOUNDS
TABLE 3.2 FUNCTIONAL GROUPS OF ORGANIC COMPOUNDS X
There are 4 major categories of organic compounds:
CarbohydratesLipidsProteinsNucleic Acids
ORGANIC COMPOUNDS
MACROMOLECULES
Carbohydrates, Lipids, Proteins and Nucleic Acids are macromolecules.
This means they are BIG molecules.
They are made of smaller molecules that serve as the building blocks.
Like a brick is the building block for a brick wall these smaller molecules combine to create the macromolecules.
ORGANIC COMPOUNDS
Smaller Molecules (Building Blocks/subunits)
= monomers
Larger Molecules
= polymers
ORGANIC COMPOUNDS
MAKING & BREAKING POLYMERS
Condensation Reaction /Dehydration Synthesis
Hydrolysis Reaction
Monomer Polymer
Remove water
Add water
DEHYDRATION SYNTHESIS
Removing water to build a polymer
HYDROLYSIS
Adding water to break down a polymer
CARBOHYDRATES Why does our body (and all
living things) need this molecule?Provides ENERGY
Where do we get this molecule?Pasta, Potatoes, Rice, Candy,
Soda, Sugar
CARBOHYDRATES
Which is the polymer and which is the monomer?
Polymer!
Monomer!
CARBOHYDRATES Monomers of carbs =
monosaccharideMono means 1, saccharide
means sugarCommon examples are:
Glucose (grains)Fructose (fruit)Galactose (milk)
FIGURE 3.4B STRUCTURES OF GLUCOSE AND FRUCTOSE
C
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H H
H
H
H
HO
H
H
H
C
O
HO
OH
OH
OH
OH
OH
OH
OH
C O
OH
Glucose Fructose
COUNT UP THE ATOMS FOR EACH
C
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H H
H
H
H
HO
H
H
H
C
O
HO
OH
OH
OH
OH
OH
OH
OH
C O
OH
Glucose Fructose
C
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H H
H
H
H
HO
H
H
H
C
O
HO
OH
OH
OH
OH
OH
OH
OH
C O
OH
Glucose Fructose
Glucose Fructose
Carbon 6 6
Hydrogen 12 12
Oxygen 6 6
ISOMERS – SAME MOLECULAR FORMULA, DIFFERENT STRUCTURAL FORMULA
C
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H H
H
H
H
HO
H
H
H
C
O
HO
OH
OH
OH
OH
OH
OH
OH
C O
OH
Glucose Fructose
FIGURE 3.4C THREE REPRESENTATIONS OF THE RING FORM OF GLUCOSE
H
H
H
H
H
H H
H
HH
O
C
C
C C
O
OH
OH HO OH
OH
CH2OH
CH2OH
C
OH
OH
O
OH
Structural formula
Abbreviated structure
Simplified structure
6
5
4
3 2
1
CARBOHYDRATES
Functional GroupsFunctional groups are groups of
atoms that give a molecule its characteristic properties.
Carbohydrates have 2 functional groups =
Hydroxyl -OH
Carbonyl -COH
CARBOHYDRATES
• Here you see 2 monosaccharides coming together to form a disaccharide.
What type of reaction is this?
_______________________________Dehydration synthesis or condensation reaction
CARBOHYDRATES
Polymers = Dissaccharide (two)
Common examples are:Sucrose - sugarMaltose – grains (beer)
Lactose - milk
Lactose
TABLE 3.6 SWEETNESS SCALE
Polysaccharide (many)Common examples are:
Starch - potatoCellulose – plant cell walls
Glycogen - animals
CARBOHYDRATES
FIGURE 3.7 POLYSACCHARIDES
Starch granules in potato tuber cells
Glycogen granules in muscle tissue
Cellulose fibrils in a plant cell wall
Glucose monomer
Cellulose molecules
STARCH
GLYCOGEN
CELLULOSE
O O
OOOOOO
O O O
O
OO
OO
OO
OO
OO
OO
O
OO
OO
OO
OO O
OOOOOO
OOOOOO
O
OH
OH
BENEDICT’S TESTFOR MONOSACCHARIDES
- +
IODINE TEST FOR POLYSACCHARIDES
MAKING & BREAKING POLYMERS
Remove WaterCondensation Reaction /Dehydration Synthesis
Monomer Polymer
Add WaterHydrolysis Reaction
LIPIDS Why does our body (and all living things)
need this molecule?Stores ENERGY Insulation & ProtectionMake up cell membranes (provide
boundaries) Where do we get this molecule?
Dairy products, Meat, Oil
LIPIDS
Triglyceride
LIPIDS Monomers
GlycerolFatty Acids
Saturated Fatty AcidsAll Single BondsFound in animalsSolid at room temperature
Unsaturated Fatty AcidsAt least 1 double or triple bondFound in plantsLiquid at room temperature
Animation
HYDROGENATED OILS To convert an oil into a solid at room
temp.Add hydrogensDecreases the number of double bonds
LIPIDS
Functional Groups = Hydroxyl Carboxyl
LIPIDS• Here you see 2
glycerol combining with a fatty acid in a dehydration reaction. This happens 3 times to create a triglyceride.
• animation
LIPIDS Polymers =
Are very diverse BUT they are all hydrophobic
Examples; Triglyceride Steroids Wax Phospholipids
FIGURE 3.9 CHOLESTEROL, A STEROID
HO
CH3
CH3
H3C CH3
CH3
A steroid – cholesterol. A molecule that is needed for cell membrane stability. Excess cholesterol due to consumption of fatty foods can lead to health problems like atherosclerosis (clogging of the arteries)
ANABOLIC STEROIDS Synthetic variants of male hormone –
testosterone Anabolism – building of substances by the
body Mimics testosterone which builds muscle
tissue
Overdosing – leads to serious side effects- depression, liver damage, shrunken
testicles, breast development
FIGURE 3.8A WATER BEADING ON THE NATURALLY OILY COATING OF FEATHERS
Drop each food sample onto a paper bag. Hold up to the light, it will turn translucent if lipids are present.
Sudan red is lipid soluble. The sudan red will stain the lipid layer. Solid red.
SUDAN RED TEST FOR LIPIDS
- +
PROTEINS Why does our body (and all
living things) need this molecule?
oMake up our structure (actin in muscles, hemoglobin and antibodies in blood, etc)
FIGURE 3.11 STRUCTURAL AND CONTRACTILE PROTEINS
PROTEINSR
ate
of r
eact
ion
Temperature (C)
0 20 40 60 80 100
Enzyme A Enzyme B
• Speed up chemical reactions (enzymes)
PROTEINS
Where do we get this molecule?Dairy products, Meat, Beans, Nuts
PROTEIN Monomers
Amino AcidsThere are only 20 different amino acids
PROTEINS
PROTEIN Functional Groups =
Amino – NH2
Carboxyl - COOH
AMINO ACID STRUCTURE
Fig. 3.14, p. 42
tyrosine (tyr) lysine (lys) glutamate (glu) glycine (gly)
UNCHARGED,POLAR AMINO ACID
POSITIVELY CHARGED,POLAR AMINO ACID
NEGATIVELY CHARGED,POLAR AMINO ACID
valine (val) phenylalanine (phe) methionine (met) proline (pro)
PROTEINS• Here you see 2 amino acids
combining in a dehydration reaction.
• Animation
Fig. 3.15, p. 43
newly formingpolypeptidechain
Onepeptidegroup
Fig. 3.17, p. 44
PROTEINS Polymers = Polypeptides
Poly means many, peptide comes from the bonding
Fig. 3.16, p. 43
disulfide bridges
PROTEINS The shape of a protein determines its
function.
Shape depends on the interaction of the R groups of each amino acid forming weak H bonds.
Because H bonds are weak they can be broken by exposure to extreme pH or temperature, and certain chemicals like salt.
When a proteins shape is altered and therefore it stops functioning correctly we say it has been denatured.
FIGURE 3.14 PROTEIN STRUCTURE – 4 LEVELSLevels of Protein Structure
Primary structureGly
ThrGly Glu
Ser Lys
Cys
ProLeu Met
Val
Lys
ValLeu Asp Ala Val Arg Gly Ser
Pro
Ala
Ile
Asn ValAla
ValHis Val
Secondary structure
C
N
O C
C
N H
O C
C
H
Hydrogenbond
O C
N HC
CO
N H
O C
C
N H
C
N
O C
C
N HO C
C
N H
CO
C
H
N H
CO
H C R
HN
Alpha helix
Amino acids
CN
H
C C
H HO
NR C C
ON
H
O
C C N
H
C C
O
N
H
O
C C NH
C
O
C N
H
O
C C N
H
C
O
O
CC
N
H
C C
O
N
H
C C
O
N
H
CC
O
N
H
CC
O
N
H
C C
O
N
H
CC
O
N
H
CC
O
H
N
C
Pleated sheet
Tertiary structure Polypeptide(single subunitof transthyretin)
Quaternary structureTransthyretin, withfour identicalPolypeptide subunits
PheArg
c) Tertiary structure of one polypeptide chain. The 3 D shape created by interactions of R groups.
A well known example is hemoglobin, which consists of 2 alpha and 2 beta chains, consisting of 141 and 146 amino acid residues respectively.
Fig. 3.18, p. 44
betachain
betachain
alphachain
hemegroup
twists andcoils in thepolypeptidechain of aglobinmolecule
alphachain
FIGURE 3.14 PROTEIN STRUCTURE – 4 LEVELSLevels of Protein Structure
GlyThr
Gly GluSer Lys
Cys
ProLeu Met
Val
Lys
ValLeu Asp Ala Val Arg Gly Ser
Pro
Ala
Ile
Asn ValAla
ValHis Val
Weak hydrogen and ionic bonds
C
N
O C
C
N H
O C
C
H
Hydrogenbond
O C
N HC
CO
N H
O C
C
N H
C
N
O C
C
N HO C
C
N H
CO
C
H
N H
CO
H C R
HN
Alpha helix
Amino acids
CN
H
C C
H HO
NR C C
ON
H
O
C C N
H
C C
O
N
H
O
C C NH
C
O
C N
H
O
C C N
H
C
O
O
CC
N
H
C C
O
N
H
C C
O
N
H
CC
O
N
H
CC
O
N
H
C C
O
N
H
CC
O
N
H
CC
O
H
N
C
Pleated sheet
Hydrogen, ionic, and disulfide bridges
Polypeptide(single subunitof transthyretin)
Not all reach this structureTransthyretin, withfour identicalPolypeptide subunits
PheArg
Covalent bonds - peptide
APPLICATION IN SCIENCE Proteins are the keys to the mysteries of
how our bodies function. Research biologists explore the shapes
of proteins and how they work A huge area of protein chemistry is in
the medical fieldAntibodies to fight infections, disease,
cancersProteins that do not function properly in
human beings with disease
http://www.ebi.ac.uk/pdbe-apps/quips?story=Sunhats
http://www.ebi.ac.uk/pdbe-apps/quips?story=XmasFactor
BIURETS TEST FOR PROTEINS
FIGURE 3.15 LINUS PAULING WITH A MODEL OF THE ALPHA HELIX IN 1948
#4) NUCLEIC ACIDS Why does our body (and all living
things) need this molecule?Stores and expresses the directions
for how to make proteinsAKA: the blueprint for life
Where do we get this molecule?We inherit this molecule from our
parents and find it in all of the foods we eat.
NUCLEIC ACIDS
NUCLEIC ACIDS
Monomers Nucleotides
3 parts
FIGURE 3.16B PART OF A POLYNUCLEOTIDE
Sugar-phosphatebackbone
T
G
C
T
A Nucleotide
FIGURE 3.16C DNA DOUBLE HELIX
C
TA
GC
C G
T A
C G
A T
A
G C
A T
A T
T A
Basepair
T
FORMING NUCLEOTIDES
… OH + H H
Short polymer Monomer
H2O
H2O
Dehydration
Hydrolysis…
Longer polymer
H
NUCLEIC ACIDS Cellular energy - ATP
NUCLEIC ACIDS Polymers =
DNA Deoxyribose Sugar Bases: A, C, G, and T
RNA Ribose Sugar Bases: A, C, G, and U